A pipeline I never wrote a line of worked flawlessly on the first try, and it left me with impostor syndrome. Here is why relying on AI agents is not cheating, but a permanent shift in what scientific expertise actually means.
Jun 23, 2026
Partial charges quietly drive the electrostatics behind every docking score. This guide compares the common semi-empirical options — AM1-BCC, PM6, AM1/PM3, Gasteiger and RESP — and gives a practical recommendation for when to use each.
Jun 23, 2026
A step-by-step, fully open-source pipeline that turns raw Protein Data Bank structures into a ligand-based 3D pharmacophore — mining the PDB, aligning binding pockets, clustering ligands, fixing bond orders, and distilling a consensus feature map ready for virtual screening.
Jun 23, 2026
I tried to reproduce the well-known PDBbind data-leakage effect with a small 3D GNN on a laptop — and couldn't. Two independent diagnostics show why: leakage only inflates models strong enough to memorize.
Jun 19, 2026
Building a QSAR model is only half the job. The harder question is: does it actually work? Overfitted models routinely pass internal checks while failing completely on new compounds. The OECD principles and decades of best-practice literature have converged on a three-tier validation framework that separates what a model has memorised from what it can genuinely predict.
Jun 1, 2026
A comprehensive walkthrough of cheminformatics, machine learning, molecular docking, ADMET prediction, and molecular dynamics simulations as the modern toolbox for computer-aided drug discovery.
May 10, 2026
A practical guide to three advanced 3D fingerprinting methods (PLEC, SPLIF, and E3FP) and how to choose between them when featurizing docking poses for ML-based drug discovery models.
Apr 1, 2026
Conceptual overview of the key energetic contributions governing protein–ligand binding in molecular docking, including desolvation, entropy, water displacement, electrostatics, and scoring function behavior.
Mar 13, 2026
Preparing a molecular system correctly before running molecular dynamics (MD) simulations is essential for obtaining meaningful and reproducible results. Small technical choices such as solvent box geometry, treatment of protein termini, and strategies for selecting representative conformations can strongly influence simulation stability, computational efficiency, and interpretation of results.
Mar 9, 2026
A practical guide to the most common methodological errors in Density Functional Theory calculations, explaining why legacy protocols like B3LYP/6-31G* are no longer reliable and how to adopt robust, modern best practices.
Dec 24, 2025